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- PDB-7moq: The structure of the Tetrahymena thermophila outer dynein arm on ... -

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Entry
Database: PDB / ID: 7moq
TitleThe structure of the Tetrahymena thermophila outer dynein arm on doublet microtubule
Components
  • (Docking complex ...) x 2
  • (Dynein light ...) x 10
  • (Outer dynein arm docking complex protein oda ...) x 2
  • Dynein heavy chain, outer arm protein
  • Dynein intermediate chain 2
  • Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative
  • Flagellar outer dynein arm intermediate protein, putative
  • Outer arm dynein beta heavy chain
  • Thioredoxin
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / cilia / doublet / axoneme / outer dynein arm / dynein
Function / homology
Function and homology information


axonemal dynein complex / outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / ciliary tip / ciliary rootlet / dynein complex / minus-end-directed microtubule motor activity ...axonemal dynein complex / outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / ciliary tip / ciliary rootlet / dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / microtubule-based movement / dynein intermediate chain binding / protein-disulfide reductase activity / microtubule-based process / cell redox homeostasis / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / cilium / ciliary basal body / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Outer dynein arm-docking complex subunit 3 / : / : / ODAD1 central coiled coil region / Dynein heavy chain 3, AAA+ lid domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / AAA+ lid domain / : ...Outer dynein arm-docking complex subunit 3 / : / : / ODAD1 central coiled coil region / Dynein heavy chain 3, AAA+ lid domain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / AAA+ lid domain / : / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Filamin/ABP280 repeat / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Thioredoxin / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / IPT/TIG domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / ig-like, plexins, transcription factors / Kelch-type beta propeller / IPT domain / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Thioredoxin domain profile. / Thioredoxin domain / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / EF-hand domain pair / Immunoglobulin E-set / WD domain, G-beta repeat / Thioredoxin-like superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / EF hand protein / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Dynein-1, subspecies f / Dynein light chain roadblock-type 2 protein ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Dynein light chain tctex-type 1 protein / Dynein intermediate chain 2 / EF hand protein / Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative / Dynein-1, subspecies f / Dynein light chain roadblock-type 2 protein / Tubulin alpha chain / Tubulin beta chain / Dynein light chain / Dynein light chain / Dynein light chain / Dynein light chain / Thioredoxin / Dynein light chain 2A / Dynein heavy chain, outer arm protein / Dynein light chain roadblock-type 2 protein / Dynein light chain / ODAD1 central coiled coil region domain-containing protein / Outer dynein arm docking complex protein oda protein / Flagellar outer dynein arm intermediate protein, putative / Dynein light chain
Similarity search - Component
Biological speciesTetrahymena thermophila CU428 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsKubo, S. / Yang, S.K. / Ichikawa, M. / Bui, K.H.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04954 Canada
Canadian Institutes of Health Research (CIHR)PJT-156354 Canada
CitationJournal: EMBO Rep / Year: 2021
Title: Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM.
Authors: Shintaroh Kubo / Shun Kai Yang / Corbin S Black / Daniel Dai / Melissa Valente-Paterno / Jacek Gaertig / Muneyoshi Ichikawa / Khanh Huy Bui /
Abstract: Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the ...Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs' conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryo-electron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with coarse-grained molecular dynamic simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex.
History
DepositionMay 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative
B: Outer arm dynein beta heavy chain
C: Dynein heavy chain, outer arm protein
D: Dynein intermediate chain 2
E: Flagellar outer dynein arm intermediate protein, putative
F: Dynein light chain roadblock-type 2 protein
G: Dynein light chain roadblock-type 2 protein
H: Dynein light chain
I: Dynein light chain
J: Dynein light chain
K: Dynein light chain
L: Dynein light chain
M: Dynein light chain
N: Dynein light chain 2A
O: Dynein light chain tctex-type 1 protein
P: Thioredoxin
Q: Tubulin beta chain
R: Tubulin alpha chain
S: Tubulin alpha chain
T: Outer dynein arm docking complex protein oda protein
U: Tubulin beta chain
V: Docking complex 1/2 protein
W: Tubulin alpha chain
X: Docking complex 1 protein
Y: Tubulin beta chain
Z: Outer dynein arm docking complex protein oda protein
d: Dynein intermediate chain 2
e: Flagellar outer dynein arm intermediate protein, putative
s: Tubulin alpha chain
u: Tubulin beta chain
r: Tubulin alpha chain
q: Tubulin beta chain
w: Tubulin alpha chain
y: Tubulin beta chain
x: Docking complex 1/2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,783,90156
Polymers2,776,59535
Non-polymers7,30621
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 7 types, 19 molecules ACDdEePQUYuqyRSWsrw

#1: Protein Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative


Mass: 475554.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7M6H4
#3: Protein Dynein heavy chain, outer arm protein


Mass: 534328.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22A67
#4: Protein Dynein intermediate chain 2


Mass: 77888.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7M008
#5: Protein Flagellar outer dynein arm intermediate protein, putative


Mass: 77178.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q23FU1
#16: Protein Thioredoxin


Mass: 12855.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFX5
#17: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49617.676 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: P41352
#18: Protein
Tubulin alpha chain / Alpha-tubulin


Mass: 49639.035 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: P41351

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Dynein light ... , 10 types, 10 molecules FGHIJKLMNO

#6: Protein Dynein light chain roadblock-type 2 protein


Mass: 14751.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7MHB1
#7: Protein Dynein light chain roadblock-type 2 protein


Mass: 18490.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22MV2
#8: Protein Dynein light chain


Mass: 10780.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFW2
#9: Protein Dynein light chain


Mass: 12348.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFX0
#10: Protein Dynein light chain


Mass: 10973.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFV9
#11: Protein Dynein light chain


Mass: 13336.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22R86
#12: Protein Dynein light chain


Mass: 12516.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: W7XJB1
#13: Protein Dynein light chain


Mass: 10453.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HFW0
#14: Protein Dynein light chain 2A


Mass: 15608.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q1HGH8
#15: Protein Dynein light chain tctex-type 1 protein


Mass: 13202.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: A4VEB3

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Outer dynein arm docking complex protein oda ... , 2 types, 2 molecules TZ

#19: Protein Outer dynein arm docking complex protein oda protein


Mass: 35237.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: I7M2C6
#22: Protein Outer dynein arm docking complex protein oda protein


Mass: 63455.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q233H6

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Docking complex ... , 2 types, 3 molecules VxX

#20: Protein Docking complex 1/2 protein


Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428
#21: Protein Docking complex 1 protein


Mass: 64756.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / References: UniProt: Q22T00

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Antibody , 1 types, 1 molecules B

#2: Antibody Outer arm dynein beta heavy chain


Mass: 530111.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / Strain: SB715 / References: UniProt: I7M9J2

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Non-polymers , 5 types, 21 molecules

#23: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#24: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#25: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#26: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#27: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Outer dynein arm complex from Tetrahymena thermophila / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#22 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: YES
Source (natural)Organism: Tetrahymena thermophila CU428 (eukaryote) / Strain: CU428 / Cellular location: cilia / Organelle: cilia
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot force 3 for 5 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: dev_3699: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.8image acquisition
4RELION3CTF correction
7UCSF Chimera1model fitting
9SPIDER19.02initial Euler assignment
10RELION3final Euler assignment
11FREALIGN9.03final Euler assignment
12FREALIGN9.03classification
13RELION33D reconstruction
14Coot0.8.7model refinement
15PHENIX1.9model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139548 / Symmetry type: POINT
Atomic model buildingB value: 179 / Protocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006132552
ELECTRON MICROSCOPYf_angle_d0.888179275
ELECTRON MICROSCOPYf_dihedral_angle_d12.19617676
ELECTRON MICROSCOPYf_chiral_restr0.0519867
ELECTRON MICROSCOPYf_plane_restr0.00523039

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